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Crystal Structure of Triple mutant (D67E, A68P, I88L) of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae at 2.3 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y7L 1Y7L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 278 0.1M HEPES, 1.3M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2 41.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.2 α = 90 b = 112.2 β = 90 c = 43.74 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2014-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.3 40.75 99.98 0.847 66.54 19.1 235300
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.382 0.781 13.29
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1Y7L 2.3 40.75 12294 575 99.951 0.173 0.171 0.1716 0.222 0.2219 32.432
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -2.135 -2.135 4.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.468 r_dihedral_angle_4_deg 17.321 r_dihedral_angle_3_deg 17.106 r_lrange_it 8.055 r_dihedral_angle_1_deg 5.764 r_scangle_it 5.151 r_mcangle_it 4.338 r_scbond_it 3.49 r_mcbond_it 2.742 r_angle_refined_deg 1.481
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.468 r_dihedral_angle_4_deg 17.321 r_dihedral_angle_3_deg 17.106 r_lrange_it 8.055 r_dihedral_angle_1_deg 5.764 r_scangle_it 5.151 r_mcangle_it 4.338 r_scbond_it 3.49 r_mcbond_it 2.742 r_angle_refined_deg 1.481 r_nbtor_refined 0.305 r_symmetry_nbd_refined 0.244 r_nbd_refined 0.208 r_symmetry_xyhbond_nbd_refined 0.139 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.107 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2319 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing